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Yorodumi- PDB-1m6o: Crystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6o | ||||||
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Title | Crystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information : / : / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / TAP binding ...: / : / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Macdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. ...Macdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2003 Title: A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition. Authors: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / ...Authors: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6o.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6o.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6o ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6o | HTTPS FTP |
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-Related structure data
Related structure data | 1n2rC 1a1nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31980.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Truncated heavy chain / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30481, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01884, UniProt: P61769*PLUS |
#3: Protein/peptide | Mass: 1090.165 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN homo sapiens. It was derived from the HLA DP alpha (DPA*0201) polypeptide chain. References: GenBank: 14602923, UniProt: Q95HB9*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 20-30% PEG 4K, 0.1M citrate, 0.2M ammonium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Macdonald, W., (2002) FEBS Lett., 527, 27. / PH range low: 5.9 / PH range high: 5.2 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 59302 / % possible obs: 96.8 % / Redundancy: 4.76 % / Rmerge(I) obs: 0.049 |
Reflection shell | Highest resolution: 1.6 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2 |
Reflection | *PLUS Redundancy: 4.8 % / Num. measured all: 282153 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A1N Resolution: 1.6→50 Å /
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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